Applied Microbiology and Biotechnology

, Volume 73, Issue 3, pp 485–494 | Cite as

Application of FISH technology for microbiological analysis: current state and prospects

  • Benedetta BottariEmail author
  • Danilo Ercolini
  • Monica Gatti
  • Erasmo Neviani


In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.


Oligonucleotide Probe Peptide Nucleic Acid Nucleic Acid Molecule rRNA Target Target Oligonucleotide Probe 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Benedetta Bottari
    • 1
    Email author
  • Danilo Ercolini
    • 2
  • Monica Gatti
    • 1
  • Erasmo Neviani
    • 1
  1. 1.Department of Genetic, Biology of Microorganisms, Anthropology, EvolutionUniversity of ParmaParmaItaly
  2. 2.Department of Food ScienceUniversity of Naples Federico IIPorticiItaly

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